Well, was just having a similar conversation with a friend, with a computer (PC) issue. During a troubleshooting process, so many things were changed there's no way to know what actually worked, if it did.
A bad OPS (or fuel supply failure) won't cause a DTC.
Back to square one. Put everything back the way you found it, at the time it quit. Change one thing at a time. Begin with the free/cheap stuff.
Free = Not throwing parts in you don't already have.
Spare PMD's = Free.
PMD extension = Free (with and w/o). Try connecting the PMD(s) to the original pump harness, first.
ESS = Free to test, disable, etc. (remove the turbo inlet pipe and have a wood block, etc. handy to shut off the air, if necessary, or a fuel valve at the inlet, or both).
Spare PCM = Free.
Another thing to add to your "free" (or almost) testing process, is the fuel supply. Use an inline filter (inexpensive gas filter is OK, for testing), place it on the outlet of your marine tank, elevate the tank (about cab-roof high), prime the line, install the line to the IP inlet. This will give you a positive fuel supply, not requiring a pump, and eliminating restriction issues. Once the problem is identified, restore the original fuel supply and verify its operation. Deal with it independently, as necessary.
Charge batteries, as necessary.
Verify Glow Plugs are getting power, and getting hot. Bypass the controller, if necessary.
Each step, one at a time, in no specific order. I would start with the fuel supply (elevated tank), then work your way through the electrical, starting with the ESS.